Examples with DataCitation edu.harvard.iq.dataverse.DataCitation used on opensource projects

Example 1 with DataCitation

use of edu.harvard.iq.dataverse.DataCitation in project dataverse by IQSS.

the class LocalSubmitToArchiveCommand method performArchiveSubmission.

@Override
public WorkflowStepResult performArchiveSubmission(DatasetVersion dv, ApiToken token, Map<String, String> requestedSettings) {
    logger.fine("In LocalCloudSubmitToArchive...");
    String localPath = requestedSettings.get(":BagItLocalPath");
    String zipName = null;
    try {
        Dataset dataset = dv.getDataset();
        if (dataset.getLockFor(Reason.finalizePublication) == null && dataset.getLockFor(Reason.FileValidationFailed) == null) {
            String spaceName = dataset.getGlobalId().asString().replace(':', '-').replace('/', '-').replace('.', '-').toLowerCase();
            DataCitation dc = new DataCitation(dv);
            Map<String, String> metadata = dc.getDataCiteMetadata();
            String dataciteXml = DOIDataCiteRegisterService.getMetadataFromDvObject(dv.getDataset().getGlobalId().asString(), metadata, dv.getDataset());
            FileUtils.writeStringToFile(new File(localPath + "/" + spaceName + "-datacite.v" + dv.getFriendlyVersionNumber() + ".xml"), dataciteXml, StandardCharsets.UTF_8);
            BagGenerator bagger = new BagGenerator(new OREMap(dv, false), dataciteXml);
            bagger.setAuthenticationKey(token.getTokenString());
            zipName = localPath + "/" + spaceName + "v" + dv.getFriendlyVersionNumber() + ".zip";
            bagger.generateBag(new FileOutputStream(zipName + ".partial"));
            File srcFile = new File(zipName + ".partial");
            File destFile = new File(zipName);
            if (srcFile.renameTo(destFile)) {
                logger.fine("Localhost Submission step: Content Transferred");
                dv.setArchivalCopyLocation("file://" + zipName);
            } else {
                logger.warning("Unable to move " + zipName + ".partial to " + zipName);
            }
        } else {
            logger.warning("Localhost Submision Workflow aborted: Dataset locked for finalizePublication, or because file validation failed");
            return new Failure("Dataset locked");
        }
    } catch (Exception e) {
        logger.warning("Failed to archive " + zipName + " : " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    return WorkflowStepResult.OK;
}

Example 2 with DataCitation

use of edu.harvard.iq.dataverse.DataCitation in project dataverse by IQSS.

the class DuraCloudSubmitToArchiveCommand method performArchiveSubmission.

@Override
public WorkflowStepResult performArchiveSubmission(DatasetVersion dv, ApiToken token, Map<String, String> requestedSettings) {
    String port = requestedSettings.get(DURACLOUD_PORT) != null ? requestedSettings.get(DURACLOUD_PORT) : DEFAULT_PORT;
    String dpnContext = requestedSettings.get(DURACLOUD_CONTEXT) != null ? requestedSettings.get(DURACLOUD_CONTEXT) : DEFAULT_CONTEXT;
    String host = requestedSettings.get(DURACLOUD_HOST);
    if (host != null) {
        Dataset dataset = dv.getDataset();
        if (dataset.getLockFor(Reason.finalizePublication) == null && dataset.getLockFor(Reason.FileValidationFailed) == null) {
            // Use Duracloud client classes to login
            ContentStoreManager storeManager = new ContentStoreManagerImpl(host, port, dpnContext);
            Credential credential = new Credential(System.getProperty("duracloud.username"), System.getProperty("duracloud.password"));
            storeManager.login(credential);
            String spaceName = dataset.getGlobalId().asString().replace(':', '-').replace('/', '-').replace('.', '-').toLowerCase();
            ContentStore store;
            try {
                /*
                     * If there is a failure in creating a space, it is likely that a prior version
                     * has not been fully processed (snapshot created, archiving completed and files
                     * and space deleted - currently manual operations done at the project's
                     * duracloud website)
                     */
                store = storeManager.getPrimaryContentStore();
                // Create space to copy archival files to
                store.createSpace(spaceName);
                DataCitation dc = new DataCitation(dv);
                Map<String, String> metadata = dc.getDataCiteMetadata();
                String dataciteXml = DOIDataCiteRegisterService.getMetadataFromDvObject(dv.getDataset().getGlobalId().asString(), metadata, dv.getDataset());
                MessageDigest messageDigest = MessageDigest.getInstance("MD5");
                try (PipedInputStream dataciteIn = new PipedInputStream();
                    DigestInputStream digestInputStream = new DigestInputStream(dataciteIn, messageDigest)) {
                    // Add datacite.xml file
                    new Thread(new Runnable() {

                        public void run() {
                            try (PipedOutputStream dataciteOut = new PipedOutputStream(dataciteIn)) {
                                dataciteOut.write(dataciteXml.getBytes(Charset.forName("utf-8")));
                                dataciteOut.close();
                            } catch (Exception e) {
                                logger.severe("Error creating datacite.xml: " + e.getMessage());
                                // TODO Auto-generated catch block
                                e.printStackTrace();
                                throw new RuntimeException("Error creating datacite.xml: " + e.getMessage());
                            }
                        }
                    }).start();
                    // Have seen Pipe Closed errors for other archivers when used as a workflow without this delay loop
                    int i = 0;
                    while (digestInputStream.available() <= 0 && i < 100) {
                        Thread.sleep(10);
                        i++;
                    }
                    String checksum = store.addContent(spaceName, "datacite.xml", digestInputStream, -1l, null, null, null);
                    logger.fine("Content: datacite.xml added with checksum: " + checksum);
                    String localchecksum = Hex.encodeHexString(digestInputStream.getMessageDigest().digest());
                    if (!checksum.equals(localchecksum)) {
                        logger.severe(checksum + " not equal to " + localchecksum);
                        return new Failure("Error in transferring DataCite.xml file to DuraCloud", "DuraCloud Submission Failure: incomplete metadata transfer");
                    }
                    // Store BagIt file
                    String fileName = spaceName + "v" + dv.getFriendlyVersionNumber() + ".zip";
                    // Add BagIt ZIP file
                    // Although DuraCloud uses SHA-256 internally, it's API uses MD5 to verify the
                    // transfer
                    messageDigest = MessageDigest.getInstance("MD5");
                    try (PipedInputStream in = new PipedInputStream();
                        DigestInputStream digestInputStream2 = new DigestInputStream(in, messageDigest)) {
                        new Thread(new Runnable() {

                            public void run() {
                                try (PipedOutputStream out = new PipedOutputStream(in)) {
                                    // Generate bag
                                    BagGenerator bagger = new BagGenerator(new OREMap(dv, false), dataciteXml);
                                    bagger.setAuthenticationKey(token.getTokenString());
                                    bagger.generateBag(out);
                                } catch (Exception e) {
                                    logger.severe("Error creating bag: " + e.getMessage());
                                    // TODO Auto-generated catch block
                                    e.printStackTrace();
                                    throw new RuntimeException("Error creating bag: " + e.getMessage());
                                }
                            }
                        }).start();
                        i = 0;
                        while (digestInputStream.available() <= 0 && i < 100) {
                            Thread.sleep(10);
                            i++;
                        }
                        checksum = store.addContent(spaceName, fileName, digestInputStream2, -1l, null, null, null);
                        logger.fine("Content: " + fileName + " added with checksum: " + checksum);
                        localchecksum = Hex.encodeHexString(digestInputStream2.getMessageDigest().digest());
                        if (!checksum.equals(localchecksum)) {
                            logger.severe(checksum + " not equal to " + localchecksum);
                            return new Failure("Error in transferring Zip file to DuraCloud", "DuraCloud Submission Failure: incomplete archive transfer");
                        }
                    } catch (RuntimeException rte) {
                        logger.severe(rte.getMessage());
                        return new Failure("Error in generating Bag", "DuraCloud Submission Failure: archive file not created");
                    }
                    logger.fine("DuraCloud Submission step: Content Transferred");
                    // Document the location of dataset archival copy location (actually the URL
                    // where you can
                    // view it as an admin)
                    StringBuffer sb = new StringBuffer("https://");
                    sb.append(host);
                    if (!port.equals("443")) {
                        sb.append(":" + port);
                    }
                    sb.append("/duradmin/spaces/sm/");
                    sb.append(store.getStoreId());
                    sb.append("/" + spaceName + "/" + fileName);
                    dv.setArchivalCopyLocation(sb.toString());
                    logger.fine("DuraCloud Submission step complete: " + sb.toString());
                } catch (ContentStoreException | IOException e) {
                    // TODO Auto-generated catch block
                    logger.warning(e.getMessage());
                    e.printStackTrace();
                    return new Failure("Error in transferring file to DuraCloud", "DuraCloud Submission Failure: archive file not transferred");
                } catch (RuntimeException rte) {
                    logger.severe(rte.getMessage());
                    return new Failure("Error in generating datacite.xml file", "DuraCloud Submission Failure: metadata file not created");
                } catch (InterruptedException e) {
                    logger.warning(e.getLocalizedMessage());
                    e.printStackTrace();
                }
            } catch (ContentStoreException e) {
                logger.warning(e.getMessage());
                e.printStackTrace();
                String mesg = "DuraCloud Submission Failure";
                if (!(1 == dv.getVersion()) || !(0 == dv.getMinorVersionNumber())) {
                    mesg = mesg + ": Prior Version archiving not yet complete?";
                }
                return new Failure("Unable to create DuraCloud space with name: " + spaceName, mesg);
            } catch (NoSuchAlgorithmException e) {
                logger.severe("MD5 MessageDigest not available!");
            }
        } else {
            logger.warning("DuraCloud Submision Workflow aborted: Dataset locked for finalizePublication, or because file validation failed");
            return new Failure("Dataset locked");
        }
        return WorkflowStepResult.OK;
    } else {
        return new Failure("DuraCloud Submission not configured - no \":DuraCloudHost\".");
    }
}

Example 3 with DataCitation

use of edu.harvard.iq.dataverse.DataCitation in project dataverse by IQSS.

the class GoogleCloudSubmitToArchiveCommand method performArchiveSubmission.

@Override
public WorkflowStepResult performArchiveSubmission(DatasetVersion dv, ApiToken token, Map<String, String> requestedSettings) {
    logger.fine("In GoogleCloudSubmitToArchiveCommand...");
    String bucketName = requestedSettings.get(GOOGLECLOUD_BUCKET);
    String projectName = requestedSettings.get(GOOGLECLOUD_PROJECT);
    logger.fine("Project: " + projectName + " Bucket: " + bucketName);
    if (bucketName != null && projectName != null) {
        Storage storage;
        try {
            FileInputStream fis = new FileInputStream(System.getProperty("dataverse.files.directory") + System.getProperty("file.separator") + "googlecloudkey.json");
            storage = StorageOptions.newBuilder().setCredentials(ServiceAccountCredentials.fromStream(fis)).setProjectId(projectName).build().getService();
            Bucket bucket = storage.get(bucketName);
            Dataset dataset = dv.getDataset();
            if (dataset.getLockFor(Reason.finalizePublication) == null) {
                String spaceName = dataset.getGlobalId().asString().replace(':', '-').replace('/', '-').replace('.', '-').toLowerCase();
                DataCitation dc = new DataCitation(dv);
                Map<String, String> metadata = dc.getDataCiteMetadata();
                String dataciteXml = DOIDataCiteRegisterService.getMetadataFromDvObject(dv.getDataset().getGlobalId().asString(), metadata, dv.getDataset());
                String blobIdString = null;
                MessageDigest messageDigest = MessageDigest.getInstance("MD5");
                try (PipedInputStream dataciteIn = new PipedInputStream();
                    DigestInputStream digestInputStream = new DigestInputStream(dataciteIn, messageDigest)) {
                    // Add datacite.xml file
                    new Thread(new Runnable() {

                        public void run() {
                            try (PipedOutputStream dataciteOut = new PipedOutputStream(dataciteIn)) {
                                dataciteOut.write(dataciteXml.getBytes(Charset.forName("utf-8")));
                                dataciteOut.close();
                            } catch (Exception e) {
                                logger.severe("Error creating datacite.xml: " + e.getMessage());
                                // TODO Auto-generated catch block
                                e.printStackTrace();
                                throw new RuntimeException("Error creating datacite.xml: " + e.getMessage());
                            }
                        }
                    }).start();
                    // Have seen broken pipe in PostPublishDataset workflow without this delay
                    int i = 0;
                    while (digestInputStream.available() <= 0 && i < 100) {
                        Thread.sleep(10);
                        i++;
                    }
                    Blob dcXml = bucket.create(spaceName + "/datacite.v" + dv.getFriendlyVersionNumber() + ".xml", digestInputStream, "text/xml", Bucket.BlobWriteOption.doesNotExist());
                    String checksum = dcXml.getMd5ToHexString();
                    logger.fine("Content: datacite.xml added with checksum: " + checksum);
                    String localchecksum = Hex.encodeHexString(digestInputStream.getMessageDigest().digest());
                    if (!checksum.equals(localchecksum)) {
                        logger.severe(checksum + " not equal to " + localchecksum);
                        return new Failure("Error in transferring DataCite.xml file to GoogleCloud", "GoogleCloud Submission Failure: incomplete metadata transfer");
                    }
                    // Store BagIt file
                    String fileName = spaceName + ".v" + dv.getFriendlyVersionNumber() + ".zip";
                    // Add BagIt ZIP file
                    // Google uses MD5 as one way to verify the
                    // transfer
                    messageDigest = MessageDigest.getInstance("MD5");
                    try (PipedInputStream in = new PipedInputStream(100000);
                        DigestInputStream digestInputStream2 = new DigestInputStream(in, messageDigest)) {
                        Thread writeThread = new Thread(new Runnable() {

                            public void run() {
                                try (PipedOutputStream out = new PipedOutputStream(in)) {
                                    // Generate bag
                                    BagGenerator bagger = new BagGenerator(new OREMap(dv, false), dataciteXml);
                                    bagger.setAuthenticationKey(token.getTokenString());
                                    bagger.generateBag(out);
                                } catch (Exception e) {
                                    logger.severe("Error creating bag: " + e.getMessage());
                                    // TODO Auto-generated catch block
                                    e.printStackTrace();
                                    try {
                                        digestInputStream2.close();
                                    } catch (Exception ex) {
                                        logger.warning(ex.getLocalizedMessage());
                                    }
                                    throw new RuntimeException("Error creating bag: " + e.getMessage());
                                }
                            }
                        });
                        writeThread.start();
                        /*
                             * The following loop handles two issues. First, with no delay, the
                             * bucket.create() call below can get started before the piped streams are set
                             * up, causing a failure (seen when triggered in a PostPublishDataset workflow).
                             * A minimal initial wait, e.g. until some bytes are available, would address
                             * this. Second, the BagGenerator class, due to it's use of parallel streaming
                             * creation of the zip file, has the characteristic that it makes a few bytes
                             * available - from setting up the directory structure for the zip file -
                             * significantly earlier than it is ready to stream file content (e.g. for
                             * thousands of files and GB of content). If, for these large datasets,
                             * bucket.create() is called as soon as bytes are available, the call can
                             * timeout before the bytes for all the zipped files are available. To manage
                             * this, the loop waits until 90K bytes are available, larger than any expected
                             * dir structure for the zip and implying that the main zipped content is
                             * available, or until the thread terminates, with all of its content written to
                             * the pipe. (Note the PipedInputStream buffer is set at 100K above - I didn't
                             * want to test whether that means that exactly 100K bytes will be available()
                             * for large datasets or not, so the test below is at 90K.)
                             * 
                             * An additional sanity check limits the wait to 2K seconds. The BagGenerator
                             * has been used to archive >120K files, 2K directories, and ~600GB files on the
                             * SEAD project (streaming content to disk rather than over an internet
                             * connection) which would take longer than 2K seconds (10+ hours) and might
                             * produce an initial set of bytes for directories > 90K. If Dataverse ever
                             * needs to support datasets of this size, the numbers here would need to be
                             * increased, and/or a change in how archives are sent to google (e.g. as
                             * multiple blobs that get aggregated) would be required.
                             */
                        i = 0;
                        while (digestInputStream2.available() <= 90000 && i < 2000 && writeThread.isAlive()) {
                            Thread.sleep(1000);
                            logger.fine("avail: " + digestInputStream2.available() + " : " + writeThread.getState().toString());
                            i++;
                        }
                        logger.fine("Bag: transfer started, i=" + i + ", avail = " + digestInputStream2.available());
                        if (i == 2000) {
                            throw new IOException("Stream not available");
                        }
                        Blob bag = bucket.create(spaceName + "/" + fileName, digestInputStream2, "application/zip", Bucket.BlobWriteOption.doesNotExist());
                        if (bag.getSize() == 0) {
                            throw new IOException("Empty Bag");
                        }
                        blobIdString = bag.getBlobId().getBucket() + "/" + bag.getBlobId().getName();
                        checksum = bag.getMd5ToHexString();
                        logger.fine("Bag: " + fileName + " added with checksum: " + checksum);
                        localchecksum = Hex.encodeHexString(digestInputStream2.getMessageDigest().digest());
                        if (!checksum.equals(localchecksum)) {
                            logger.severe(checksum + " not equal to " + localchecksum);
                            return new Failure("Error in transferring Zip file to GoogleCloud", "GoogleCloud Submission Failure: incomplete archive transfer");
                        }
                    } catch (RuntimeException rte) {
                        logger.severe("Error creating Bag during GoogleCloud archiving: " + rte.getMessage());
                        return new Failure("Error in generating Bag", "GoogleCloud Submission Failure: archive file not created");
                    }
                    logger.fine("GoogleCloud Submission step: Content Transferred");
                    // Document the location of dataset archival copy location (actually the URL
                    // where you can
                    // view it as an admin)
                    StringBuffer sb = new StringBuffer("https://console.cloud.google.com/storage/browser/");
                    sb.append(blobIdString);
                    dv.setArchivalCopyLocation(sb.toString());
                } catch (RuntimeException rte) {
                    logger.severe("Error creating datacite xml file during GoogleCloud Archiving: " + rte.getMessage());
                    return new Failure("Error in generating datacite.xml file", "GoogleCloud Submission Failure: metadata file not created");
                }
            } else {
                logger.warning("GoogleCloud Submision Workflow aborted: Dataset locked for pidRegister");
                return new Failure("Dataset locked");
            }
        } catch (Exception e) {
            logger.warning(e.getLocalizedMessage());
            e.printStackTrace();
            return new Failure("GoogleCloud Submission Failure", e.getLocalizedMessage() + ": check log for details");
        }
        return WorkflowStepResult.OK;
    } else {
        return new Failure("GoogleCloud Submission not configured - no \":GoogleCloudBucket\"  and/or \":GoogleCloudProject\".");
    }
}

Example 4 with DataCitation

use of edu.harvard.iq.dataverse.DataCitation in project dataverse by IQSS.

the class Access method datafileBundle.

// @EJB
// TODO:
// versions? -- L.A. 4.0 beta 10
@Path("datafile/bundle/{fileId}")
@GET
@Produces({ "application/zip" })
public BundleDownloadInstance datafileBundle(@PathParam("fileId") String fileId, @QueryParam("fileMetadataId") Long fileMetadataId, @QueryParam("gbrecs") boolean gbrecs, @QueryParam("key") String apiToken, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/
{
    GuestbookResponse gbr = null;
    DataFile df = findDataFileOrDieWrapper(fileId);
    if (apiToken == null || apiToken.equals("")) {
        apiToken = headers.getHeaderString(API_KEY_HEADER);
    }
    // This will throw a ForbiddenException if access isn't authorized:
    checkAuthorization(df, apiToken);
    if (gbrecs != true && df.isReleased()) {
        // Write Guestbook record if not done previously and file is released
        User apiTokenUser = findAPITokenUser(apiToken);
        gbr = guestbookResponseService.initAPIGuestbookResponse(df.getOwner(), df, session, apiTokenUser);
        guestbookResponseService.save(gbr);
        MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, df);
        mdcLogService.logEntry(entry);
    }
    DownloadInfo dInfo = new DownloadInfo(df);
    BundleDownloadInstance downloadInstance = new BundleDownloadInstance(dInfo);
    FileMetadata fileMetadata = null;
    if (fileMetadataId == null) {
        fileMetadata = df.getFileMetadata();
    } else {
        fileMetadata = dataFileService.findFileMetadata(fileMetadataId);
    }
    downloadInstance.setFileCitationEndNote(new DataCitation(fileMetadata).toEndNoteString());
    downloadInstance.setFileCitationRIS(new DataCitation(fileMetadata).toRISString());
    downloadInstance.setFileCitationBibtex(new DataCitation(fileMetadata).toBibtexString());
    ByteArrayOutputStream outStream = null;
    outStream = new ByteArrayOutputStream();
    Long dfId = df.getId();
    try {
        ddiExportService.exportDataFile(dfId, outStream, null, null, fileMetadataId);
        downloadInstance.setFileDDIXML(outStream.toString());
    } catch (Exception ex) {
    // if we can't generate the DDI, it's ok;
    // we'll just generate the bundle without it.
    }
    return downloadInstance;
}

Example 5 with DataCitation

use of edu.harvard.iq.dataverse.DataCitation in project dataverse by IQSS.

the class DataCiteExporter method exportDataset.

@Override
public void exportDataset(DatasetVersion version, JsonObject json, OutputStream outputStream) throws ExportException {
    try {
        DataCitation dc = new DataCitation(version);
        Map<String, String> metadata = dc.getDataCiteMetadata();
        String xml = DOIDataCiteRegisterService.getMetadataFromDvObject(version.getDataset().getGlobalId().asString(), metadata, version.getDataset());
        outputStream.write(xml.getBytes(Charset.forName("utf-8")));
    } catch (IOException e) {
        throw new ExportException("Caught IOException performing DataCite export");
    }
}